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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.25.1

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/sarek analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2025-07-08, 12:41 EDT based on data in: /sc/arion/projects/NGSCRC/Work/Seqera/ba/fb9db1d6241bd7fe6c1c4fa100fcdb

        Because this report contains a lot of samples, you may need to click 'Show plot' to see some graphs.

        General Statistics

        Showing 1504 samples.

        Created with MultiQC

        Bcftools

        Utilities for variant calling and manipulating VCFs and BCFs.URL: https://samtools.github.io/bcftoolsDOI: 10.1093/gigascience/giab008

        Variant Substitution Types

        Created with MultiQC

        Variant Quality

        Created with MultiQC

        Indel Distribution

        Created with MultiQC

        Variant depths

        Read depth support distribution for called variants

        Created with MultiQC

        Vcftools

        Program to analyse and reporting on VCF files.URL: https://vcftools.github.ioDOI: 10.1093/bioinformatics/btr330

        TsTv by Count

        Plot of TSTV-BY-COUNT - the transition to transversion ratio as a function of alternative allele count from the output of vcftools TsTv-by-count.

        Transition is a purine-to-purine or pyrimidine-to-pyrimidine point mutations. Transversion is a purine-to-pyrimidine or pyrimidine-to-purine point mutation. Alternative allele count is the number of alternative alleles at the site. Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.) Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on --TsTv-by-count

        Created with MultiQC

        TsTv by Qual

        Plot of TSTV-BY-QUAL - the transition to transversion ratio as a function of SNP quality from the output of vcftools TsTv-by-qual.

        Transition is a purine-to-purine or pyrimidine-to-pyrimidine point mutations. Transversion is a purine-to-pyrimidine or pyrimidine-to-purine point mutation. Quality here is the Phred-scaled quality score as given in the QUAL column of VCF. Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.) Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on --TsTv-by-qual

        Created with MultiQC

        SNPeff

        Annotates and predicts the effects of variants on genes (such as amino acid changes).URL: http://snpeff.sourceforge.netDOI: 10.4161/fly.19695

        Variants by Genomic Region

        The stacked bar plot shows locations of detected variants in the genome and the number of variants for each location.

        The upstream and downstream interval size to detect these genomic regions is 5000bp by default.

        Created with MultiQC

        Variant Effects by Impact

        The stacked bar plot shows the putative impact of detected variants and the number of variants for each impact.

        There are four levels of impacts predicted by SnpEff:

        • High: High impact (like stop codon)
        • Moderate: Middle impact (like same type of amino acid substitution)
        • Low: Low impact (ie silence mutation)
        • Modifier: No impact
        Created with MultiQC

        Variants by Effect Types

        The stacked bar plot shows the effect of variants at protein level and the number of variants for each effect type.

        This plot shows the effect of variants with respect to the mRNA.

        Created with MultiQC

        Variants by Functional Class

        The stacked bar plot shows the effect of variants and the number of variants for each effect type.

        This plot shows the effect of variants on the translation of the mRNA as protein. There are three possible cases:

        • Silent: The amino acid does not change.
        • Missense: The amino acid is different.
        • Nonsense: The variant generates a stop codon.
        Created with MultiQC

        Variant Qualities

        The line plot shows the quantity as function of the variant quality score.

        The quality score corresponds to the QUAL column of the VCF file. This score is set by the variant caller.

        Created with MultiQC

        VEP

        Determines the effect of variants on genes, transcripts and protein sequences, as well as regulatory regions.URL: https://www.ensembl.org/info/docs/tools/vep/index.htmlDOI: 10.1186/s13059-016-0974-4

        General Statistics

        Table showing general statistics of VEP annotation run

        Showing 1504 samples.

        Created with MultiQC

        Variant classes

        Classes of variants found in the data.

        Created with MultiQC

        Consequences

        Predicted consequences of variations.

        Created with MultiQC

        SIFT summary

        SIFT variant effect prediction.

        Created with MultiQC

        PolyPhen summary

        PolyPhen variant effect prediction.

        Created with MultiQC

        Variants by chromosome

        Number of variants found on each chromosome.

        Created with MultiQC

        Position in protein

        Relative position of affected amino acids in protein.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        ASCATalleleCounter4.3.0
        ascat3.1.1
        ASSESS_SIGNIFICANCEcontrolfreec11.6
        BCFTOOLS_SORTbcftools1.2
        BCFTOOLS_STATSbcftools1.2
        CALCULATECONTAMINATIONgatk44.5.0.0
        CNNSCOREVARIANTSgatk44.5.0.0
        CNVKIT_BATCHcnvkit0.9.10
        samtools1.17
        CNVKIT_CALLcnvkit0.9.10
        CNVKIT_EXPORTcnvkit0.9.10
        CNVKIT_GENEMETRICScnvkit0.9.10
        ENSEMBLVEP_VEPensemblvep113.0
        FILTERMUTECTCALLSgatk44.5.0.0
        FILTERVARIANTTRANCHESgatk44.5.0.0
        FREEBAYESfreebayes1.3.6
        FREEC2BEDcontrolfreec11.6b
        FREEC2CIRCOScontrolfreec11.6b
        FREEC_SOMATICcontrolfreec11.6b
        FREEC_TUMORONLYcontrolfreec11.6b
        GATK4_HAPLOTYPECALLERgatk44.5.0.0
        GETPILEUPSUMMARIESgatk44.5.0.0
        GETPILEUPSUMMARIES_NORMALgatk44.5.0.0
        GETPILEUPSUMMARIES_TUMORgatk44.5.0.0
        LEARNREADORIENTATIONMODELgatk44.5.0.0
        MAKEGRAPH2controlfreec11.6b
        MSISENSORPRO_MSISOMATICmsisensor-pro1.2.0
        MUTECT2gatk44.5.0.0
        MUTECT2_PAIREDgatk44.5.0.0
        SAMTOOLS_MPILEUPsamtools1.21
        SNPEFF_SNPEFFsnpeff5.1d
        STRELKA_SINGLEstrelka2.9.10
        STRELKA_SOMATICstrelka2.9.10
        SVDB_MERGEbcftools1.21
        svdb2.8.2
        TABIX_BGZIPTABIXtabix1.2
        TABIX_BGZIP_TIDDIT_SVtabix1.2
        TABIX_TABIXtabix1.2
        TABIX_VC_FREEBAYEStabix1.2
        TIDDIT_SVtiddit3.6.1
        VCFTOOLS_TSTV_COUNTvcftools0.1.16
        WorkflowNextflow24.04.4
        nf-core/sarekv3.5.0-gae4dd11

        nf-core/sarek Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/sarek

        Methods

        Data was processed using nf-core/sarek v3.5.0 (doi: 10.12688/f1000research.16665.2), (doi: 10.1093/nargab/lqae031), (doi: 10.5281/zenodo.3476425) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v24.04.4 (Di Tommaso et al., 2017) with the following command:

        nextflow run 'https://github.com/nf-core/sarek' -name NRG-GY003_crams_7 -params-file 'https://api.cloud.seqera.io/ephemeral/d_hgo10DXjlnM1AB_iAS8w.json' -with-tower 'https://api.cloud.seqera.io' -r ae4dd11acc8b7e13fd6d4d45a92ff29a8e2b958d -profile singularity -resume aa0889b3-2262-4c90-8eff-62054a9be265

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        nf-core/sarek Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/sarek

        Input/output options

        input
        https://api.cloud.seqera.io/workspaces/26890372228482/datasets/3GfOwU6YBVYUh66oxmoIth/v/1/n/NRG-GY003_WES_cram.csv
        outdir
        /sc/arion/projects/NGSCRC/Work/Seqera/NRG-GY003_All_Varcalls
        step
        variant_calling

        Main options

        intervals
        /sc/arion/projects/NGSCRC/Resources/Twist_Bioscience_Comprehensive_Exome_Targets/Twist_Comprehensive_Exome_Covered_Targets_hg38.sorted.padded.merged.bed
        tools
        freebayes,tiddit,cnvkit,ascat,msisensorpro,mutect2,controlfreec,haplotypecaller,strelka,snpeff,vep,merge
        wes
        true

        Variant Calling

        cf_chrom_len
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len
        joint_mutect2
        true
        pon
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz
        pon_tbi
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi

        Annotation

        vep_version
        113.0-0

        Reference genome options

        ascat_alleles
        /sc/arion/projects/NGSCRC/Resources/ASCAT_WES/battenberg_alleles_on_target_hg38.zip
        ascat_genome
        hg38
        ascat_loci
        /sc/arion/projects/NGSCRC/Resources/ASCAT_WES/battenberg_loci_on_target_hg38.zip
        ascat_loci_gc
        /sc/arion/projects/NGSCRC/Resources/ASCAT_WES/GC_G1000_on_target_hg38.zip
        ascat_loci_rt
        /sc/arion/projects/NGSCRC/Resources/ASCAT_WES/RT_G1000_on_target_hg38.zip
        bwa
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/
        bwamem2
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/
        chr_dir
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes
        dbsnp
        /sc/arion/projects/NGSCRC/Resources/gatk_hg38/gatk_bundle_2024/Homo_sapiens_assembly38.dbsnp138.vcf
        dbsnp_tbi
        /sc/arion/projects/NGSCRC/Resources/gatk_hg38/gatk_bundle_2024/Homo_sapiens_assembly38.dbsnp138.vcf.idx
        dbsnp_vqsr
        --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz
        dict
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
        dragmap
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/dragmap/
        fasta
        /sc/arion/projects/NGSCRC/Resources/gatk_hg38/gatk_bundle_2024/Homo_sapiens_assembly38.fasta
        fasta_fai
        /sc/arion/projects/NGSCRC/Resources/gatk_hg38/gatk_bundle_2024/Homo_sapiens_assembly38.fasta.fai
        germline_resource
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz
        germline_resource_tbi
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi
        known_indels
        /sc/arion/projects/NGSCRC/Resources/gatk_hg38/gatk_bundle_2024/Homo_sapiens_assembly38.known_indels.vcf.gz
        known_indels_tbi
        /sc/arion/projects/NGSCRC/Resources/gatk_hg38/gatk_bundle_2024/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi
        known_indels_vqsr
        --resource:gatk,known=false,training=true,truth=true,prior=10.0 Homo_sapiens_assembly38.known_indels.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
        known_snps
        /sc/arion/projects/NGSCRC/Resources/gatk_hg38/gatk_bundle_2024/1000G_phase1.snps.high_confidence.hg38.vcf.gz
        known_snps_tbi
        /sc/arion/projects/NGSCRC/Resources/gatk_hg38/gatk_bundle_2024/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi
        known_snps_vqsr
        --resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_omni2.5.hg38.vcf.gz
        mappability
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem
        ngscheckmate_bed
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed
        sentieon_dnascope_model
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model
        snpeff_cache
        /sc/arion/projects/NGSCRC/Resources/SnpEff
        snpeff_db
        GRCh38.105
        vep_cache
        /sc/arion/projects/NGSCRC/Resources/VEP
        vep_cache_version
        113
        vep_genome
        GRCh38
        vep_species
        homo_sapiens

        Core Nextflow options

        configFiles
        N/A
        containerEngine
        singularity
        launchDir
        /sc/arion/projects/NGSCRC/Work/Seqera
        profile
        singularity
        projectDir
        /sc/arion/projects/NGSCRC/Work/Seqera/.nextflow/pipelines/f83b9b1a/nf-core/sarek
        revision
        3.5.0
        runName
        NRG-GY003_crams_7
        userName
        monsok03
        workDir
        /sc/arion/projects/NGSCRC/Work/Seqera

        MultiQC v1.25.1 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.